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      Classification of autochthonous dengue virus type 1 strains circulating in Japan in 2014

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          Abstract

          In this paper, we classify by representativeness the elements of a set of complete genomic sequences of Dengue Virus Type 1 (DENV-1), corresponding to the outbreak in Japan during 2014. The set is coming from four regions: Chiba, Hyogo, Shizuoka and Tokyo. We consider this set as composed of independent samples coming from Markovian processes of finite order and finite alphabet. Under the assumption of the existence of a law that prevails in at least 50% of the samples of the set, we identify the sequences governed by the predominant law (see [ 1, 2]). The rule of classification is based on a local metric between samples, which tends to zero when we compare sequences of identical law and tends to infinity when comparing sequences with different laws. We found that the order of representativeness, from highest to lowest and according to the origin of the sequences is: Tokyo, Chiba, Hyogo, and Shizuoka. When comparing the Japanese sequences with their contemporaries from Asia, we find that the less representative sequence (from Shizuoka) is positioned in groups considerably far away from that which includes the sequences from the other regions in Japan, this offers evidence to suppose that the outbreak in Japan could be produced by more than one type of DENV-1.

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          Estimating the Dimension of a Model

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            Direct sequencing and characterization of a clinical isolate of Epstein-Barr virus from nasopharyngeal carcinoma tissue by using next-generation sequencing technology.

            Epstein-Barr virus (EBV)-encoded molecules have been detected in the tumor tissues of several cancers, including nasopharyngeal carcinoma (NPC), suggesting that EBV plays an important role in tumorigenesis. However, the nature of EBV with respect to genome width in vivo and whether EBV undergoes clonal expansion in the tumor tissues are still poorly understood. In this study, next-generation sequencing (NGS) was used to sequence DNA extracted directly from the tumor tissue of a patient with NPC. Apart from the human sequences, a clinically isolated EBV genome 164.7 kb in size was successfully assembled and named GD2 (GenBank accession number HQ020558). Sequence and phylogenetic analyses showed that GD2 was closely related to GD1, a previously assembled variant derived from a patient with NPC. GD2 contains the most prevalent EBV variants reported in Cantonese patients with NPC, suggesting that it might be the prevalent strain in this population. Furthermore, GD2 could be grouped into a single subtype according to common classification criteria and contains only 6 heterozygous point mutations, suggesting the monoclonal expansion of GD2 in NPC. This study represents the first genome-wide analysis of a clinical isolate of EBV directly extracted from NPC tissue. Our study reveals that NGS allows the characterization of genome-wide variations of EBV in clinical tumors and provides evidence of monoclonal expansion of EBV in vivo. The pipeline could also be applied to the study of other pathogen-related malignancies. With additional NGS studies of NPC, it might be possible to uncover the potential causative EBV variant involved in NPC.
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              DNA sequence and expression of the B95-8 Epstein—Barr virus genome

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                Author and article information

                Contributors
                Role: Guest Editor
                Journal
                fopen
                https://www.4open-sciences.org
                4open
                4open
                EDP Sciences
                2557-0250
                03 July 2019
                03 July 2019
                2019
                : 2
                : ( publisher-idID: fopen/2019/01 )
                Affiliations
                [1 ] Department of Mathematics, Federal University of Technology, , Av. Monteiro Lobato, s/n – Km 04, Campus Ponta Grossa, Ponta Grossa, CEP 84016-210 Paraná, Brazil,
                [2 ] Department of Statistics, University of Campinas, , Sergio Buarque de Holanda, 651, Campinas, CEP 13083-859 São Paulo, Brazil,
                Author notes
                [* ]Corresponding author: marcoscordeiro@ 123456utfpr.edu.br
                Article
                fopen190012
                10.1051/fopen/2019018
                © M.T.A. Cordeiro et al., Published by EDP Sciences, 2019

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Counts
                Figures: 3, Tables: 5, Equations: 43, References: 10, Pages: 8
                Product
                Self URI (journal page): https://www.4open-sciences.org/
                Categories
                Mathematics - Applied Mathematics
                Research Article
                Statistical Inference in Copula Models and Markov Processes, Case Studies and Insights
                Custom metadata
                4open 2019, 2, 20
                2019
                2019
                2019

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